Hi Jan-Philip,
Thanks for the response. I visually inspected the system and side chain of one residue is almost
out of the box.
Senthil
Huhu,
just to be sure that this is not an "issue of wrong perspective": did
you quantify the minimum distance between the complex and the box? How
big is it, if not 8 Angstrom?
Jan-Philip
On 11/08/2011 06:24 PM, Senthil Natesan wrote:
> Dear Amber Users,
>
> Greetings.
>
> I am trying to solvateOCT a protein-ligand complex, but the minimum distance between
> the complex and the solvent box edge seems to be not holding at the expected level (8 A)
> The protein-ligand complex is almost touching the box edge (pls see the attached image)
> though I get the proper solvation with solvateBox.
>
>
> The command used is
>
>
> solvateOct complex TIP3PBOX 8.0
>
> I am not sure what is wrong ? your suggestions/comments will be appreciated.
>
> thanks,
> Senthil Natesan
>
>
>
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Received on Tue Nov 08 2011 - 10:30:05 PST
